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Open Access 01-11-2013 | Original Paper

Deep sequencing reveals increased DNA methylation in chronic rat epilepsy

Authors: Katja Kobow, Antony Kaspi, K. N. Harikrishnan, Katharina Kiese, Mark Ziemann, Ishant Khurana, Ina Fritzsche, Jan Hauke, Eric Hahnen, Roland Coras, Angelika Mühlebner, Assam El-Osta, Ingmar Blümcke

Published in: Acta Neuropathologica | Issue 5/2013

Abstract

Epilepsy is a frequent neurological disorder, although onset and progression of seizures remain difficult to predict in affected patients, irrespective of their epileptogenic condition. Previous studies in animal models as well as human epileptic brain tissue revealed a remarkably diverse pattern of gene expression implicating epigenetic changes to contribute to disease progression. Here we mapped for the first time global DNA methylation patterns in chronic epileptic rats and controls. Using methyl-CpG capture associated with massive parallel sequencing (Methyl-Seq) we report the genomic methylation signature of the chronic epileptic state. We observed a predominant increase, rather than loss of DNA methylation in chronic rat epilepsy. Aberrant methylation patterns were inversely correlated with gene expression changes using mRNA sequencing from same animals and tissue specimens. Administration of a ketogenic, high-fat, low-carbohydrate diet attenuated seizure progression and ameliorated DNA methylation mediated changes in gene expression. This is the first report of unsupervised clustering of an epigenetic mark being used in epilepsy research to separate epileptic from non-epileptic animals as well as from animals receiving anti-convulsive dietary treatment. We further discuss the potential impact of epigenetic changes as a pathogenic mechanism of epileptogenesis.

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NCBI Resource Coordinators (2013) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 41:D8–D20CrossRef

Ageta-Ishihara N, Takemoto-Kimura S, Nonaka M, Adachi-Morishima A, Suzuki K, Kamijo S, Fujii H, Mano T, Blaeser F, Chatila TA, Mizuno H, Hirano T, Tagawa Y, Okuno H, Bito H et al (2009) Control of cortical axon elongation by a GABA-driven Ca2+/calmodulin-dependent protein kinase cascade. J Neurosci 29:13720–13729PubMedCrossRef

Allis CD, Jenuwein T, Reinberg D, Caparros M-L (eds) (2007) Epigenetics. Cold Spring Harbor Laboratory Press Cold Spring Harbor, New York

Becker AJ, Chen J, Zien A, Sochivko D, Normann S, Schramm J, Elger CE, Wiestler OD, Blumcke I et al (2003) Correlated stage- and subfield-associated hippocampal gene expression patterns in experimental and human temporal lobe epilepsy. Eur J Neurosci 18:2792–2802PubMedCrossRef

Becker AJ, Pitsch J, Sochivko D, Opitz T, Staniek M, Chen CC, Campbell KP, Schoch S, Yaari Y, Beck H et al (2008) Transcriptional upregulation of Cav3.2 mediates epileptogenesis in the pilocarpine model of epilepsy. J Neurosci 28:13341–13353PubMedCrossRef

Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Stat Soc Ser B (Methodol) 57:289–300

Blumcke I, Coras R, Miyata H, Ozkara C et al (2012) Defining clinico-neuropathological subtypes of mesial temporal lobe epilepsy with hippocampal sclerosis. Brain Pathol 22:402–411PubMedCrossRef

Blumcke I, Pauli E, Clusmann H, Schramm J, Becker A, Elger C, Merschhemke M, Meencke HJ, Lehmann T, von Deimling A, Scheiwe C, Zentner J, Volk B, Romstock J, Stefan H, Hildebrandt M et al (2007) A new clinico-pathological classification system for mesial temporal sclerosis. Acta Neuropathol 113:235–244PubMedCrossRef

Blumcke I, Thom M, Aronica E, Armstrong DD, Bartolomei F, Bernasconi A, Bernasconi N, Bien CG, Cendes F, Coras R, Cross JH, Jacques TS, Kahane P, Mathern GW, Miyata H, Moshe SL, Oz B, Ozkara C, Perucca E, Sisodiya S, Wiebe S, Spreafico R et al (2013) International consensus classification of hippocampal sclerosis in temporal lobe epilepsy: a task force report from the ILAE Commission on diagnostic methods. Epilepsia 54(7):1315–1329PubMedCrossRef

10.

Bough KJ, Wetherington J, Hassel B, Pare JF, Gawryluk JW, Greene JG, Shaw R, Smith Y, Geiger JD, Dingledine RJ et al (2006) Mitochondrial biogenesis in the anticonvulsant mechanism of the ketogenic diet. Ann Neurol 60:223–235PubMedCrossRef

11.

Brinkman AB, Gu H, Bartels SJ, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG et al (2012) Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res 22:1128–1138PubMedCrossRef

12.

Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG et al (2010) Whole-genome DNA methylation profiling using MethylCap-seq. Methods 52:232–236PubMedCrossRef

13.

Cross JH (2013) New research with diets and epilepsy. J Child Neurol 28:970–974PubMedCrossRef

14.

Crowe SL, Tsukerman S, Gale K, Jorgensen TJ, Kondratyev AD et al (2011) Phosphorylation of histone H2A.X as an early marker of neuronal endangerment following seizures in the adult rat brain. J Neurosci 31:7648–7656PubMedCrossRef

15.

Deaton AM, Webb S, Kerr AR, Illingworth RS, Guy J, Andrews R, Bird A et al (2011) Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Res 21:1074–1086PubMedCrossRef

16.

Elliott RC, Miles MF, Lowenstein DH (2003) Overlapping microarray profiles of dentate gyrus gene expression during development- and epilepsy-associated neurogenesis and axon outgrowth. J Neurosci 23:2218–2227PubMed

17.

ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M et al (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74PubMedCrossRef

18.

Feil R, Fraga MF (2012) Epigenetics and the environment: emerging patterns and implications. Nat Rev Genet 13:97–109PubMed

19.

Feng J, Zhou Y, Campbell SL, Le T, Li E, Sweatt JD, Silva AJ, Fan G et al (2010) Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat Neurosci 13:423–430PubMedCrossRef

20.

Fischer A, Sananbenesi F, Wang X, Dobbin M, Tsai LH et al (2007) Recovery of learning and memory is associated with chromatin remodelling. Nature 447:178–182PubMedCrossRef

21.

Garriga-Canut M, Schoenike B, Qazi R, Bergendahl K, Daley TJ, Pfender RM, Morrison JF, Ockuly J, Stafstrom C, Sutula T, Roopra A et al (2006) 2-Deoxy-d-glucose reduces epilepsy progression by NRSF-CtBP-dependent metabolic regulation of chromatin structure. Nat Neurosci 9:1382–1387PubMedCrossRef

22.

Gorter JA, van Vliet EA, Aronica E, Breit T, Rauwerda H, Lopes da Silva FH, Wadman WJ et al (2006) Potential new antiepileptogenic targets indicated by microarray analysis in a rat model for temporal lobe epilepsy. J Neurosci 26:11083–11110PubMedCrossRef

23.

Greene RW (2011) Adenosine: front and center in linking nutrition and metabolism to neuronal activity. J Clin Invest 121:2548–2550PubMedCrossRef

24.

Hagarman JA, Motley MP, Kristjansdottir K, Soloway PD (2013) Coordinate regulation of DNA methylation and H3K27me3 in mouse embryonic stem cells. PLoS One 8:e53880PubMedCrossRef

25.

Harikrishnan KN, Bayles R, Ciccotosto GD, Maxwell S, Cappai R, Pelka GJ, Tam PP, Christodoulou J, El-Osta A et al (2010) Alleviating transcriptional inhibition of the norepinephrine slc6a2 transporter gene in depolarized neurons. J Neurosci 30:1494–1501PubMedCrossRef

26.

Hendriksen H, Datson NA, Ghijsen WE, van Vliet EA, da Silva FH, Gorter JA, Vreugdenhil E et al (2001) Altered hippocampal gene expression prior to the onset of spontaneous seizures in the rat post-status epilepticus model. Eur J Neurosci 14:1475–1484PubMedCrossRef

27.

da Huang W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57CrossRef

28.

Huang Y, Doherty JJ, Dingledine R (2002) Altered histone acetylation at glutamate receptor 2 and brain-derived neurotrophic factor genes is an early event triggered by status epilepticus. J Neurosci 22:8422–8428PubMed

29.

Huang Y, Myers SJ, Dingledine R (1999) Transcriptional repression by REST: recruitment of Sin3A and histone deacetylase to neuronal genes. Nat Neurosci 2:867–872PubMedCrossRef

30.

Jia YH, Zhu X, Li SY, Ni JH, Jia HT et al (2006) Kainate exposure suppresses activation of GluR2 subunit promoter in primary cultured cerebral cortical neurons through induction of RE1-silencing transcription factor. Neurosci Lett 403:103–108PubMedCrossRef

31.

Jimenez-Mateos EM, Engel T, Merino-Serrais P, McKiernan RC, Tanaka K, Mouri G, Sano T, O’Tuathaigh C, Waddington JL, Prenter S, Delanty N, Farrell MA, O’Brien DF, Conroy RM, Stallings RL, Defelipe J, Henshall DC et al (2012) Silencing microRNA-134 produces neuroprotective and prolonged seizure-suppressive effects. Nat Med 18:1087–1094PubMedCrossRef

32.

Kan AA, de Jager W, de Wit M, Heijnen C, van Zuiden M, Ferrier C, van Rijen P, Gosselaar P, Hessel E, van Nieuwenhuizen O, de Graan PN et al (2012) Protein expression profiling of inflammatory mediators in human temporal lobe epilepsy reveals co-activation of multiple chemokines and cytokines. J Neuroinflamm 9:207CrossRef

33.

Kobow K, Auvin S, Jensen F, Loscher W, Mody I, Potschka H, Prince D, Sierra A, Simonato M, Pitkanen A, Nehlig A, Rho JM et al (2012) Finding a better drug for epilepsy: antiepileptogenesis targets. Epilepsia 53:1868–1876PubMedCrossRef

34.

Kobow K, Blumcke I (2011) The methylation hypothesis: do epigenetic chromatin modifications play a role in epileptogenesis? Epilepsia 52(Suppl 4):15–19PubMedCrossRef

35.

Kobow K, Blumcke I (2012) The emerging role of DNA methylation in epileptogenesis. Epilepsia 53(Suppl 9):11–20PubMedCrossRef

36.

Kobow K, Jeske I, Hildebrandt M, Hauke J, Hahnen E, Buslei R, Buchfelder M, Weigel D, Stefan H, Kasper B, Pauli E, Blumcke I et al (2009) Increased reelin promoter methylation is associated with granule cell dispersion in human temporal lobe epilepsy. J Neuropathol Exp Neurol 68:356–364PubMedCrossRef

37.

Kokubo M, Nishio M, Ribar TJ, Anderson KA, West AE, Means AR et al (2009) BDNF-mediated cerebellar granule cell development is impaired in mice null for CaMKK2 or CaMKIV. J Neurosci 29:8901–8913PubMedCrossRef

38.

Kossoff EH, Hartman AL (2012) Ketogenic diets: new advances for metabolism-based therapies. Curr Opin Neurol 25:173–178PubMedCrossRef

39.

Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA et al (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645PubMedCrossRef

40.

Lemke JR, Riesch E, Scheurenbrand T, Schubach M, Wilhelm C, Steiner I, Hansen J, Courage C, Gallati S, Burki S, Strozzi S, Simonetti BG, Grunt S, Steinlin M, Alber M, Wolff M, Klopstock T, Prott EC, Lorenz R, Spaich C, Rona S, Lakshminarasimhan M, Kroll J, Dorn T, Kramer G, Synofzik M, Becker F, Weber YG, Lerche H, Bohm D, Biskup S et al (2012) Targeted next generation sequencing as a diagnostic tool in epileptic disorders. Epilepsia 53:1387–1398PubMedCrossRef

41.

Levenson JM, Roth TL, Lubin FD, Miller CA, Huang IC, Desai P, Malone LM, Sweatt JD et al (2006) Evidence that DNA (cytosine-5) methyltransferase regulates synaptic plasticity in the hippocampus. J Biol Chem 281:15763–15773PubMedCrossRef

42.

Levenson JM, Sweatt JD (2005) Epigenetic mechanisms in memory formation. Nat Rev Neurosci 6:108–118PubMedCrossRef

43.

Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760PubMedCrossRef

44.

Liu M, Sheng Z, Cai L, Zhao K, Tian Y, Fei J et al (2012) Neuronal conditional knockout of NRSF decreases vulnerability to seizures induced by pentylenetetrazol in mice. Acta Biochim Biophys Sin 44:476–482PubMedCrossRef

45.

Lukasiuk K, Dabrowski M, Adach A, Pitkanen A et al (2006) Epileptogenesis-related genes revisited. Prog Brain Res 158:223–241PubMedCrossRef

46.

Margueron R, Reinberg D (2011) The Polycomb complex PRC2 and its mark in life. Nature 469:343–349PubMedCrossRef

47.

Martinowich K, Hattori D, Wu H, Fouse S, He F, Hu Y, Fan G, Sun YE et al (2003) DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation. Science 302:890–893PubMedCrossRef

48.

Masino SA, Kawamura M Jr, Ruskin DN, Geiger JD, Boison D et al (2012) Purines and neuronal excitability: links to the ketogenic diet. Epilepsy Res 100:229–238PubMedCrossRef

49.

Masino SA, Li T, Theofilas P, Sandau US, Ruskin DN, Fredholm BB, Geiger JD, Aronica E, Boison D et al (2011) A ketogenic diet suppresses seizures in mice through adenosine A receptors. J Clin Invest 121:2679–2683PubMedCrossRef

50.

Masino SA, Rho JM (2012) Mechanisms of ketogenic diet action. In: Noebels JL, Avoli M, Rogawski MA, Olsen RW, Delgado-Escueta AV (eds) Jasper’s basic mechanisms of the epilepsies (contemporary neurology series). Oxford University Press, Oxford, pp 1003–1024CrossRef

51.

McClelland S, Flynn C, Dubé C, Richichi C, Zha Q, Ghestem A, Esclapez M, Bernard C, Baram TZ et al (2011) Neuron-restrictive silencer factor-mediated hyperpolarization-activated cyclic nucleotide gated channelopathy in experimental temporal lobe epilepsy. Ann Neurol 70:454–464PubMedCrossRef

52.

Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O’Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE et al (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553–560PubMedCrossRef

53.

Miller-Delaney SF, Das S, Sano T, Jimenez-Mateos EM, Bryan K, Buckley PG, Stallings RL, Henshall DC et al (2012) Differential DNA methylation patterns define status epilepticus and epileptic tolerance. J Neurosci 32:1577–1588PubMedCrossRef

54.

Neal EG, Chaffe H, Schwartz RH, Lawson MS, Edwards N, Fitzsimmons G, Whitney A, Cross JH et al (2008) The ketogenic diet for the treatment of childhood epilepsy: a randomised controlled trial. Lancet Neurol 7:500–506PubMedCrossRef

55.

Okano M, Bell DW, Haber DA, Li E et al (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99:247–257PubMedCrossRef

56.

Peters M, Mizuno K, Ris L, Angelo M, Godaux E, Giese KP et al (2003) Loss of Ca2+/calmodulin kinase kinase beta affects the formation of some, but not all, types of hippocampus-dependent long-term memory. J Neurosci 23:9752–9760PubMed

57.

Pirola L, Balcerczyk A, Tothill RW, Haviv I, Kaspi A, Lunke S, Ziemann M, Karagiannis T, Tonna S, Kowalczyk A, Beresford-Smith B, Macintyre G, Kelong M, Hongyu Z, Zhu J, El-Osta A et al (2011) Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells. Genome Res 21:1601–1615PubMedCrossRef

58.

Pitkanen A, Lukasiuk K (2011) Mechanisms of epileptogenesis and potential treatment targets. Lancet Neurol 10:173–186PubMedCrossRef

59.

Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842PubMedCrossRef

60.

Qureshi IA, Mehler MF (2010) Epigenetic mechanisms underlying human epileptic disorders and the process of epileptogenesis. Neurobiol Dis 39:53–60PubMedCrossRef

61.

Racine RJ (1972) Modification of seizure activity by electrical stimulation. II. Motor seizure. Electroencephalogr Clin Neurophysiol 32:281–294PubMedCrossRef

62.

Racioppi L, Means AR (2012) Calcium/calmodulin-dependent protein kinase kinase 2: roles in signaling and pathophysiology. J Biol Chem 287:31658–31665PubMedCrossRef

63.

Rho JM, Sankar R (2008) The ketogenic diet in a pill: is this possible? Epilepsia 49(Suppl 8):127–133PubMedCrossRef

64.

Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140PubMedCrossRef

65.

Robinson MD, Oshlack A (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11:R25PubMedCrossRef

66.

Rush M, Appanah R, Lee S, Lam LL, Goyal P, Lorincz MC et al (2009) Targeting of EZH2 to a defined genomic site is sufficient for recruitment of Dnmt3a but not de novo DNA methylation. Epigenetics 4:404–414PubMedCrossRef

67.

Sati S, Tanwar VS, Kumar KA, Patowary A, Jain V, Ghosh S, Ahmad S, Singh M, Reddy SU, Chandak GR, Raghunath M, Sivasubbu S, Chakraborty K, Scaria V, Sengupta S et al (2012) High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region. PLoS One 7:e31621PubMedCrossRef

68.

Shimazu T, Hirschey MD, Newman J, He W, Shirakawa K, Le Moan N, Grueter CA, Lim H, Saunders LR, Stevens RD, Newgard CB, Farese RV Jr, de Cabo R, Ulrich S, Akassoglou K, Verdin E et al (2013) Suppression of oxidative stress by beta-hydroxybutyrate, an endogenous histone deacetylase inhibitor. Science 339:211–214PubMedCrossRef

69.

Sng JC, Taniura H, Yoneda Y (2006) Histone modifications in kainate-induced status epilepticus. Eur J Neurosci 23:1269–1282PubMedCrossRef

70.

Sterner DE, Berger SL (2000) Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev 64:435–459PubMedCrossRef

71.

Strle K, Zhou JH, Shen WH, Broussard SR, Johnson RW, Freund GG, Dantzer R, Kelley KW et al (2001) Interleukin-10 in the brain. Crit Rev Immunol 21:427–449PubMedCrossRef

72.

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102:15545–15550PubMedCrossRef

73.

Tsankova NM, Kumar A, Nestler EJ (2004) Histone modifications at gene promoter regions in rat hippocampus after acute and chronic electroconvulsive seizures. J Neurosci 24:5603–5610PubMedCrossRef

74.

Vezzani A, French J, Bartfai T, Baram TZ et al (2011) The role of inflammation in epilepsy. Nat Rev Neurol 7:31–40PubMedCrossRef

75.

Vire E, Brenner C, Deplus R, Blanchon L, Fraga M, Didelot C, Morey L, Van Eynde A, Bernard D, Vanderwinden J-M, Bollen M, Esteller M, Di Croce L, de Launoit Y, Fuks F et al (2006) The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439:871–874PubMedCrossRef

76.

Ward H, Vigues S, Poole S, Bristow AF et al (2001) The rat interleukin 10 receptor: cloning and sequencing of cDNA coding for the alpha-chain protein sequence, and demonstration by western blotting of expression in the rat brain. Cytokine 15:237–240PubMedCrossRef

77.

Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D et al (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39:457–466PubMedCrossRef

78.

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS et al (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9:R137PubMedCrossRef

79.

Zhu Q, Wang L, Zhang Y, Zhao FH, Luo J, Xiao Z, Chen GJ, Wang XF et al (2011) Increased expression of DNA methyltransferase 1 and 3a in human temporal lobe epilepsy. J Mol Neurosci 46:420–426PubMedCrossRef

Title: Deep sequencing reveals increased DNA methylation in chronic rat epilepsy
Authors: Katja Kobow
Antony Kaspi
K. N. Harikrishnan
Katharina Kiese
Mark Ziemann
Ishant Khurana
Ina Fritzsche
Jan Hauke
Eric Hahnen
Roland Coras
Angelika Mühlebner
Assam El-Osta
Ingmar Blümcke
Publication date: 01-11-2013
Publisher: Springer Berlin Heidelberg
Published in: Acta Neuropathologica / Issue 5/2013
Print ISSN: 0001-6322
Electronic ISSN: 1432-0533
DOI: https://doi.org/10.1007/s00401-013-1168-8

Keynote webinar | Spotlight on medication adherence

Springer Medicine

Deep sequencing reveals increased DNA methylation in chronic rat epilepsy

Abstract

Keynote webinar | Spotlight on medication adherence

Springer Medicine

Abstract

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